Contacts of the helix formed by residues 67 - 81 (chain C) in PDB entry 1EAK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C ASN* 1.3 86.7 + - + +
68C PHE* 1.3 113.9 + - + +
69C VAL 2.9 1.9 + - - -
70C LEU* 2.9 14.9 + - - +
71C LYS* 3.1 11.4 + - + +
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Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ASN 3.6 0.4 + - - -
67C LEU* 1.3 103.0 - - + +
69C VAL* 1.3 57.4 + - + +
71C LYS* 3.6 28.2 - - + +
72C ASP* 2.7 44.5 + - - +
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C CYS* 3.9 16.4 - - - -
61C PRO* 4.5 10.1 - - + -
64C SER* 3.7 30.3 - - - +
66C ASN 3.8 7.4 - - - +
67C LEU 2.9 2.4 + - - -
68C PHE* 1.3 71.5 - - + +
70C LEU* 1.3 62.9 + - - +
71C LYS 3.1 1.3 - - - -
72C ASP* 4.2 4.0 - - - +
73C THR* 2.9 40.7 + - - +
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LYS* 4.5 22.0 - - + -
50C ALA* 5.3 0.2 - - + -
51C VAL* 5.0 8.5 - - + -
54C LEU* 3.3 27.4 - - + -
65C CYS* 4.1 20.4 - - - +
66C ASN* 3.7 24.6 + - - +
67C LEU 2.9 10.1 + - - +
69C VAL* 1.3 79.5 - - - +
71C LYS* 1.3 57.7 + - - +
73C THR* 4.6 0.7 - - - -
74C LEU* 2.8 55.0 + - + +
89C LEU* 4.8 14.1 - - + -
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Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU* 3.1 11.9 + - + +
68C PHE* 3.6 29.2 + - + +
70C LEU* 1.3 77.6 - - - +
72C ASP* 1.3 102.3 + - - +
74C LEU* 3.4 2.3 + - - +
75C LYS* 3.2 44.1 + - - +
86C THR 5.2 0.9 - - - +
87C GLY* 3.3 30.0 - - - +
88C ASP* 4.8 4.3 - - - +
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Residues in contact with ASP 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C PHE* 2.7 30.1 + - - +
69C VAL* 4.2 4.5 - - - +
71C LYS* 1.3 98.8 + - - +
73C THR* 1.3 62.7 + - - +
75C LYS* 3.3 17.9 + - - +
76C LYS* 3.3 22.6 + - - +
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Residues in contact with THR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU* 3.8 19.3 - - + -
58C TYR* 3.6 33.2 + - + +
60C CYS* 3.7 20.3 - - + +
69C VAL* 2.9 27.0 + - - +
70C LEU 4.2 1.1 - - - -
72C ASP* 1.3 73.6 - - - +
74C LEU* 1.3 67.9 + - - +
75C LYS 3.0 0.9 - - - -
76C LYS* 2.7 29.1 + - + +
77C MET* 3.2 7.6 + - - +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ALA* 4.8 2.2 - - + -
54C LEU* 3.6 22.9 - - + -
70C LEU* 2.8 53.6 + - + +
71C LYS 3.6 4.7 - - - +
73C THR* 1.3 73.3 - - - +
75C LYS* 1.3 56.3 + - - +
77C MET* 3.3 5.9 + - - +
78C GLN* 2.9 40.6 + - + +
87C GLY 3.2 24.7 - - - +
88C ASP* 3.8 17.0 - - - +
89C LEU* 3.8 26.2 - - + +
93C THR* 4.4 9.9 - - - +
97C MET* 4.9 2.5 - - + -
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C LYS* 3.2 29.9 + - - +
72C ASP* 3.4 21.8 + - - +
73C THR 2.8 4.0 + - - -
74C LEU* 1.3 71.9 - - - +
76C LYS* 1.3 59.1 + - - +
77C MET 3.0 2.0 - - - -
78C GLN* 3.0 8.6 - - - +
79C LYS* 2.9 30.0 + - - +
85C GLN* 3.5 37.2 - - + +
86C THR 4.3 2.7 + - - +
87C GLY* 3.3 26.0 - - - +
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C TYR* 3.8 20.6 + - + -
72C ASP 3.4 15.5 - - - +
73C THR* 2.7 21.6 + - - +
75C LYS* 1.3 72.9 - - - +
77C MET* 1.3 57.3 - - - +
79C LYS* 3.7 8.8 - - - +
80C PHE* 3.1 25.8 + - - +
107C VAL* 3.7 31.1 - - + +
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Residues in contact with MET 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TYR* 4.2 6.3 - - + -
54C LEU* 3.8 9.4 - - + -
58C TYR* 1.7 58.1 - - + +
73C THR 3.2 1.0 + - - +
74C LEU* 3.3 10.5 - - + +
76C LYS* 1.3 77.4 - - - +
78C GLN* 1.3 81.2 + - - +
80C PHE* 3.1 2.8 + - - +
81C PHE* 3.1 34.3 + - + -
83C LEU* 4.4 3.4 - - + -
93C THR* 4.0 11.0 - - - +
96C THR* 3.8 19.3 - - - +
97C MET* 3.3 38.4 - - + -
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Residues in contact with GLN 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 2.9 30.7 + - - +
75C LYS* 3.0 17.3 + - - +
77C MET* 1.3 83.4 - - - +
79C LYS* 1.3 61.3 + - - +
81C PHE 3.5 0.2 + - - -
82C GLY 3.0 2.8 + - - -
83C LEU* 2.6 60.4 + - + +
84C PRO 3.7 16.0 + - - +
85C GLN* 4.1 5.2 - - - -
86C THR* 3.8 0.9 + - - -
87C GLY* 3.1 24.1 + - - +
88C ASP 3.3 24.5 + - - +
90C ASP* 3.6 4.8 + - - -
93C THR* 3.3 15.2 - - + +
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Residues in contact with LYS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LYS 2.9 18.5 + - - +
76C LYS* 3.7 8.3 - - - +
78C GLN* 1.3 78.4 - - - +
80C PHE* 1.3 59.1 + - - +
82C GLY* 2.7 22.7 + - - +
83C LEU 4.8 0.2 - - - -
85C GLN* 3.1 37.8 + - - +
415C GLN* 3.8 9.4 - - - +
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Residues in contact with PHE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C TYR* 4.6 2.7 - + + +
76C LYS 3.1 12.9 + - - +
77C MET* 3.3 12.8 - - - +
79C LYS* 1.3 81.3 - - - +
81C PHE* 1.3 77.4 + + + +
82C GLY 3.4 1.6 + - - -
106C ASP* 3.8 33.9 - - + -
107C VAL* 6.4 0.7 - - + -
413C HIS* 4.0 22.7 - - + -
414C SER 3.6 26.0 - - - -
415C GLN* 3.4 49.9 - - + +
423C PRO* 3.8 20.2 - - + -
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Residues in contact with PHE 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TYR* 3.8 15.3 - + - -
58C TYR* 3.3 20.4 - - - -
77C MET* 3.1 32.9 + - + +
80C PHE* 1.3 86.7 - + - +
82C GLY* 1.3 65.9 + - - +
83C LEU* 3.2 21.4 + - + +
96C THR* 4.7 9.6 - - + +
101C ARG* 3.2 13.9 - - - -
106C ASP* 3.2 24.0 - - - -
415C GLN 6.0 0.2 - - - -
423C PRO* 3.4 23.6 - - + -
424C ILE* 3.7 22.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il